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- EMDB-19153: M. tuberculosis bacterial proteasome activator Bpa with bound sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-19153
TitleM. tuberculosis bacterial proteasome activator Bpa with bound substrate
Map data
Sample
  • Complex: M. tuberculosis bacterial proteasome activator Bpa with bound substrate
    • Protein or peptide: Bacterial proteasome activator
    • Protein or peptide: heat shock protein transcriptional repressor HspR
Keywordsprotein degradation / quality control / proteasomal activator / mycobacteria / CHAPERONE
Function / homology
Function and homology information


proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome binding / peptidoglycan-based cell wall / protein homooligomerization / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Bacterial proteasome activator / Bacterial proteasome activator / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Probable heat shock protein transcriptional repressor HspR (MerR family) / Bacterial proteasome activator
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZdanowicz R / von Rosen T / Afanasyev P / Boehringer D / Glockshuber R / Weber-Ban E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa.
Authors: Tatjana von Rosen / Rafal Zdanowicz / Yasser El Hadeg / Pavel Afanasyev / Daniel Boehringer / Alexander Leitner / Rudi Glockshuber / Eilika Weber-Ban /
Abstract: Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host ...Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.
History
DepositionDec 14, 2023-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19153.png

Downloads & links

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Map

FileDownload / File: emd_19153.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 200 pix.
= 204. Å		1.02 Å/pix.
x 200 pix.
= 204. Å		1.02 Å/pix.
x 200 pix.
= 204. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-0.8480338 - 1.4717971
Average (Standard dev.)0.009215111 (±0.064340636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_19153_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19153_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19153_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : M. tuberculosis bacterial proteasome activator Bpa with bound sub...

EntireName: M. tuberculosis bacterial proteasome activator Bpa with bound substrate
Components
  • Complex: M. tuberculosis bacterial proteasome activator Bpa with bound substrate
    • Protein or peptide: Bacterial proteasome activator
    • Protein or peptide: heat shock protein transcriptional repressor HspR

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Supramolecule #1: M. tuberculosis bacterial proteasome activator Bpa with bound sub...

SupramoleculeName: M. tuberculosis bacterial proteasome activator Bpa with bound substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: Bacterial proteasome activator

MacromoleculeName: Bacterial proteasome activator / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SLTDLVEQPA KVMRIGTMIK QLLEEVRAAP LDEASRNRLR DIHATSIREL EDGLAPELRE ELDRLTLPFN EDAVPSDAEL RIAQAQLVGW LEGLFHGIQT ALFA

UniProtKB: Bacterial proteasome activator

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Macromolecule #2: heat shock protein transcriptional repressor HspR

MacromoleculeName: heat shock protein transcriptional repressor HspR / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAKNPKDGES RTFLISVAAE LAGMHAQTLR TYDRLGLVSP RRTSGGGRRY SLHDVELLRQ VQHLSQDEGV NLAGIKRIIE LTSQVEALQS RLQEMAEELA VLRANQRREV AVVPKST

UniProtKB: Probable heat shock protein transcriptional repressor HspR (MerR family)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC Ab-Initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 469948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5lfj


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Bacterial proteasome activator Bpa

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